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Correct source identity and metabolic-relay graph claims (batch93) #1754

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311 changes: 107 additions & 204 deletions docs/communities/Rammelsberg_Cobalt_Nickel_Tailings.html
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109 changes: 82 additions & 27 deletions docs/communities/Rhizorhabdus_Cupriavidus_BDE47_Degradation_SynCom.html
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Expand Up @@ -590,7 +590,7 @@ <h2>Ecological Interactions</h2>
<div class="network-tooltip" id="network-tooltip" role="status" aria-live="polite"></div>
<svg id="network-svg" role="img" aria-labelledby="network-svg-title network-svg-desc">
<title id="network-svg-title">Ecological interaction network for Rhizorhabdus-Cupriavidus BDE-47 Degradation SynCom</title>
<desc id="network-svg-desc">Bipartite graph where circle nodes represent taxa and each ecological interaction is drawn as a distinct non-circular symbol, with colour repeating the same distinction (cross-feeding, syntrophy).</desc>
<desc id="network-svg-desc">Bipartite graph where circle nodes represent taxa and each ecological interaction is drawn as a distinct non-circular symbol, with colour repeating the same distinction (cross-feeding).</desc>
</svg>
<div class="network-legend">
<div class="legend-item">
Expand All @@ -603,8 +603,8 @@ <h2>Ecological Interactions</h2>
</div>
<div class="legend-item">
<svg class="legend-symbol" width="14" height="14" viewBox="-9 -9 18 18"
aria-hidden="true" data-symbol="symbolTriangle"
data-color="#7f30cf"></svg> Syntrophy
aria-hidden="true" data-symbol="symbolTriangle2"
data-color="#929caa"></svg> Other
</div>
</div>
</div>
Expand Down Expand Up @@ -645,7 +645,7 @@ <h3>YL-JM2C BDE-47 initiation</h3>
<strong>Downstream Effects:</strong>

<div class="flow-item">
<span class="flow-arrow">→</span> JMP134 2,4-dibromophenol rescue
<span class="flow-arrow">→</span> JMP134 2,4-dibromophenol conversion
<p class="prewrap causal-description">YL-JM2C-generated 2,4-dibromophenol is subsequently converted to 3,5-dibromocatechol by JMP134 TfdB.</p>
</div>

Expand Down Expand Up @@ -688,17 +688,20 @@ <h4>Evidence</h4>

<div class="interaction-card">
<div class="interaction-header">
<h3>JMP134 2,4-dibromophenol rescue</h3>
<span class="interaction-type">SYNTROPHY</span>
<h3>JMP134 2,4-dibromophenol conversion</h3>
</div>
<p class="prewrap interaction-description">Cupriavidus necator JMP134 hydroxylase TfdB converts the YL-JM2C dead-end 2,4-dibromophenol product to 3,5-dibromocatechol, linking YL-JM2C&#39;s initial BDE-47 attack to the downstream ortho-cleavage pathway shared by both strains.</p>
<p class="prewrap interaction-description">Cupriavidus necator JMP134 hydroxylase TfdB converts the YL-JM2C dead-end 2,4-dibromophenol product to 3,5-dibromocatechol, linking YL-JM2C&#39;s initial BDE-47 attack to the downstream ortho-cleavage pathway shared by both strains. This is the recipient conversion step in the diffusible cross-feeding relay, not evidence of a reverse metabolite transfer or improved YL-JM2C fitness. Both strains having a downstream pathway does not demonstrate exchange of 3,5-DBC back to YL-JM2C.</p>


<p><strong>Source Taxon:</strong> Cupriavidus necator JMP134</p>


<p><strong>Participating Taxa:</strong>

Rhizorhabdus wittichii YL-JM2C,

Cupriavidus necator JMP134

<p><strong>Target Taxon:</strong> Rhizorhabdus wittichii YL-JM2C</p>
</p>



Expand All @@ -721,8 +724,8 @@ <h3>JMP134 2,4-dibromophenol rescue</h3>
<strong>Downstream Effects:</strong>

<div class="flow-item">
<span class="flow-arrow">→</span> Consortium BDE-47 removal
<p class="prewrap causal-description">Removal of the 2,4-DBP bottleneck connects the two isolate pathways and enables community-level BDE-47 degradation.</p>
<span class="flow-arrow">→</span> Consortium BDE-47 removal without 2,4-DBP accumulation
<p class="prewrap causal-description">JMP134 conversion of the YL-JM2C-derived 2,4-DBP prevents that intermediate from accumulating during consortium treatment. It is not required for disappearance of the parent BDE-47, which also occurred in the YL-JM2C monoculture.</p>
</div>

</div>
Expand Down Expand Up @@ -764,10 +767,9 @@ <h4>Evidence</h4>

<div class="interaction-card">
<div class="interaction-header">
<h3>Consortium BDE-47 removal</h3>
<span class="interaction-type">SYNTROPHY</span>
<h3>Consortium BDE-47 removal without 2,4-DBP accumulation</h3>
</div>
<p class="prewrap interaction-description">The mixed YL-JM2C/JMP134 consortium removes BDE-47 from minimal salts medium, releases bromide during low-concentration BDE-47 degradation, and fully removes BDE-47 from several amended real-wastewater microcosms.</p>
<p class="prewrap interaction-description">The mixed YL-JM2C/JMP134 consortium removes BDE-47 from minimal salts medium, releases bromide during low-concentration BDE-47 degradation, and fully removes BDE-47 from several amended real-wastewater microcosms. In the direct comparison, both the mixed culture and YL-JM2C alone removed BDE-47 within 20 hours, but only the monoculture accumulated stoichiometric 2,4-DBP. The consortium therefore clears this intermediate as well as the parent. Pathway reconstruction and bromide release support catabolism, not an empirical closed carbon balance or demonstrated donor-feedback benefit.</p>



Expand Down Expand Up @@ -889,7 +891,7 @@ <h2>Associated Datasets</h2>
</section>

<section id="discussions">
<h2>Knowledge gaps &amp; discussions <span class="muted">(1)</span></h2>
<h2>Knowledge gaps &amp; discussions <span class="muted">(2)</span></h2>

<div class="discussion">
<h3>
Expand Down Expand Up @@ -924,6 +926,56 @@ <h3>

</div>

<div class="discussion">
<h3>
<span class="role-badge">KNOWLEDGE_GAP</span>
<span class="role-badge">OPEN</span>
Does clearing 2,4-DBP feed back on YL-JM2C metabolism or fitness, and what is the carbon fate?
</h3>
<p class="prewrap">The main-text monoculture comparison and transwell experiment support diffusible intermediate cross-feeding. Parent disappearance occurs in YL-JM2C alone, while the partner prevents2,4-DBP accumulation. Current SYNTROPHY does not assert obligacy; the unresolved criterion is product-removal feedback making the donor metabolism more favourable. The demonstrated relay, functional enzymes, sequential growth and positive wastewater endpoints remain. They do not independently establish reciprocal fitness, return transfer of3,5-DBC or a closed carbon balance. Preserve the pre-existing image-panel curation task; this review did not inspect supplement pixels. Non-graph SYNTROPHIC_PARTNER roles remain for issue1753.</p>

<p class="muted small">Attaches to: <code>ecological_interactions#YL-JM2C BDE-47 initiation</code>, <code>ecological_interactions#JMP134 2,4-dibromophenol conversion</code>, <code>ecological_interactions#Consortium BDE-47 removal without 2,4-DBP accumulation</code></p>



<details class="evidence-list">
<summary class="muted small">2 evidence item(s)</summary>

<div class="evidence">
<div class="evidence-head">
<span class="badge small">IN_VITRO</span>
<span class="badge small">SUPPORT</span>



<a href="https://pubmed.ncbi.nlm.nih.gov/42364169/" rel="nofollow noreferrer">PMID:42364169</a>


</div>
<p class="snippet small prewrap">when strain YL-JM2C was inoculated alone, BDE-47 disappeared within 20 h but accompanying by stoichiometric accumulation of 2,4-DBP.</p>
<p class="muted small prewrap">Main-text contrast distinguishes parent removal from clearance of the intermediate.</p>
</div>

<div class="evidence">
<div class="evidence-head">
<span class="badge small">IN_VITRO</span>
<span class="badge small">SUPPORT</span>



<a href="https://pubmed.ncbi.nlm.nih.gov/42364169/" rel="nofollow noreferrer">PMID:42364169</a>


</div>
<p class="snippet small prewrap">this metabolic relay is mediated by cross-feeding of diffusible metabolites rather than direct physical contact.</p>
<p class="muted small prewrap">Transwell interpretation supports the positive cross-feeding relay, not reverse exchange or donor-feedback fitness.</p>
</div>

</details>


</div>

</section>

<!-- Environmental Factors -->
Expand Down Expand Up @@ -1428,7 +1480,7 @@ <h4 style="color: var(--text);">Evidence</h4>

(function() {
var intId = "interaction:1";
var intType = "SYNTROPHY";
var intType = "UNKNOWN";
var metabolites = [];

var processes = [];
Expand All @@ -1441,7 +1493,7 @@ <h4 style="color: var(--text);">Evidence</h4>

nodes.push({
id: intId,
label: "JMP134 2,4-dibromophenol rescue",
label: "JMP134 2,4-dibromophenol conversion",
type: "interaction",
interactionType: intType,
metabolites: metabolites,
Expand All @@ -1450,23 +1502,26 @@ <h4 style="color: var(--text);">Evidence</h4>
});


var srcKey = "Cupriavidus necator JMP134";
if (taxonNodeIds[srcKey]) {
links.push({ source: taxonNodeIds[srcKey], target: intId });
}


var participantKeys = [

var tgtKey = "Rhizorhabdus wittichii YL-JM2C";
if (taxonNodeIds[tgtKey]) {
links.push({ source: intId, target: taxonNodeIds[tgtKey] });
}
"Rhizorhabdus wittichii YL-JM2C",

"Cupriavidus necator JMP134"

];
participantKeys.forEach(function(key) {
if (taxonNodeIds[key]) {
links.push({ source: taxonNodeIds[key], target: intId });
}
});

})();

(function() {
var intId = "interaction:2";
var intType = "SYNTROPHY";
var intType = "UNKNOWN";
var metabolites = [];

var processes = [];
Expand All @@ -1479,7 +1534,7 @@ <h4 style="color: var(--text);">Evidence</h4>

nodes.push({
id: intId,
label: "Consortium BDE-47 removal",
label: "Consortium BDE-47 removal without 2,4-DBP accumulation",
type: "interaction",
interactionType: intType,
metabolites: metabolites,
Expand Down
60 changes: 55 additions & 5 deletions docs/communities/Rhodococcus_Pseudomonas_PPOW_Consortium.html
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Expand Up @@ -680,7 +680,7 @@ <h2>Ecological Interactions</h2>
<h3>PPOW aliphatic-aromatic division of labor</h3>
<span class="interaction-type">NICHE_PARTITIONING</span>
</div>
<p class="prewrap interaction-description">The PPOW SynCom was interpreted as a functionally complementary consortium in which R. opacus DSM 43250 drives long-chain C10-C28 alkane degradation while the two Pseudomonas members contribute aromatic catabolism and solvent-stress tolerance. The source leaves the exact mechanism unresolved, so this is modeled at community scope.</p>
<p class="prewrap interaction-description">HYPOTHESIZED: The PPOW SynCom was interpreted as a functionally complementary consortium in which R. opacus DSM 43250 drives long-chain C10-C28 alkane degradation while the two Pseudomonas members contribute aromatic catabolism and solvent-stress tolerance. The source leaves the exact mechanism unresolved, so this is modeled at community scope. Bulk removal and respiratory measurements are positive community observations, not direct member-resolved substrate allocation or metabolite exchange. The source also contradicts itself about abiotic and heat-killed controls, so the causal interpretation remains PARTIAL.</p>



Expand Down Expand Up @@ -741,7 +741,7 @@ <h4>Evidence</h4>
<a href="https://pubmed.ncbi.nlm.nih.gov/42491060/"
class="pmid-link" target="_blank" rel="noopener noreferrer">PMID:42491060</a>

- SUPPORT (IN_VITRO)
- PARTIAL (IN_VITRO)
</div>

<div class="snippet">"Rhodococcus opacus DSM 43250 serves as the principal driver for long-chain alkane (C10-C28) degradation"</div>
Expand All @@ -754,7 +754,7 @@ <h4>Evidence</h4>
<a href="https://pubmed.ncbi.nlm.nih.gov/42491060/"
class="pmid-link" target="_blank" rel="noopener noreferrer">PMID:42491060</a>

- SUPPORT (IN_VITRO)
- PARTIAL (IN_VITRO)
</div>

<div class="snippet">"P. putida KT2440 targets aromatic fractions, while Pseudomonas sp. VLB120 confers significant solvent tolerance"</div>
Expand All @@ -767,7 +767,7 @@ <h4>Evidence</h4>
<a href="https://pubmed.ncbi.nlm.nih.gov/42491060/"
class="pmid-link" target="_blank" rel="noopener noreferrer">PMID:42491060</a>

- SUPPORT (IN_VITRO)
- PARTIAL (IN_VITRO)
</div>

<div class="snippet">"Although the specific mechanism remains unclear, we infer that the high degradation efficiency achieved in this study stems from rational functional complementarity among the consortium members"</div>
Expand Down Expand Up @@ -797,7 +797,7 @@ <h4>Evidence</h4>
<!-- Associated Datasets -->

<section id="discussions">
<h2>Knowledge gaps &amp; discussions <span class="muted">(1)</span></h2>
<h2>Knowledge gaps &amp; discussions <span class="muted">(2)</span></h2>

<div class="discussion">
<h3>
Expand Down Expand Up @@ -860,6 +860,56 @@ <h3>

</div>

<div class="discussion">
<h3>
<span class="role-badge">CONTROVERSY</span>
<span class="role-badge">OPEN</span>
How should the contradictory primary-source reporting of abiotic and heat-killed controls be reconciled?
</h3>
<p class="prewrap">Methods2.4 reports heat-killed controls and subtraction of abiotic removal, whereas the conclusion says these controls are lacking. Retain the reported positive bulk-removal result while flagging the unresolved source inconsistency; do not claim either adequately established control performance or complete control absence. The existing member-mechanism gap remains open, and inferred cross-feeding is not promoted to a directed edge. The abstract/main-text concentration-unit discrepancy is separately tracked under issue1753.</p>

<p class="muted small">Attaches to: <code>ecological_interactions#PPOW aliphatic-aromatic division of labor</code></p>



<details class="evidence-list">
<summary class="muted small">2 evidence item(s)</summary>

<div class="evidence">
<div class="evidence-head">
<span class="badge small">IN_VITRO</span>
<span class="badge small">SUPPORT</span>



<a href="https://pubmed.ncbi.nlm.nih.gov/42491060/" rel="nofollow noreferrer">PMID:42491060</a>


</div>
<p class="snippet small prewrap">heat-killed controls were prepared by autoclaving the inoculum</p>
<p class="muted small prewrap">Methods2.4 says heat-killed controls were included; this conflicts with the conclusion.</p>
</div>

<div class="evidence">
<div class="evidence-head">
<span class="badge small">IN_VITRO</span>
<span class="badge small">SUPPORT</span>



<a href="https://pubmed.ncbi.nlm.nih.gov/42491060/" rel="nofollow noreferrer">PMID:42491060</a>


</div>
<p class="snippet small prewrap">We acknowledge that this study lacks abiotic and heat-killed controls</p>
<p class="muted small prewrap">The conclusion contradicts Methods2.4; neither statement alone resolves actual control performance.</p>
</div>

</details>


</div>

</section>

<!-- Environmental Factors -->
Expand Down
29 changes: 29 additions & 0 deletions history/records/Rammelsberg_Cobalt_Nickel_Tailings/2026-10-07T152512Z-codex-a8ec64.yaml
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@@ -0,0 +1,29 @@
history_version: 1
target:
kind: record
path: kb/communities/Rammelsberg_Cobalt_Nickel_Tailings.yaml
slug: Rammelsberg_Cobalt_Nickel_Tailings
session:
id: 2026-10-07T152512Z-codex-a8ec64
timestamp: '2026-10-07T15:25:12Z'
actors:
- type: ai_agent
name: codex
model: unspecified
agent_tool: codex
links:
issues:
- https://github.com/CultureBotAI/CommunityMech/issues/1750
events:
- type: EDIT
outcome: changed
sections:
- interactions
- discussions
summary: Re-evidence community iron oxidation and retain the source-backed mineral-dissolution
direction without COMMENSALISM, iron-transport misannotation or rate-limiting inference.;
Re-evidence positive bulk/concentrate metal recovery using the exact Rammelsberg DOI;
remove MUTUALISM and two unproven partner-specific recycling arrows.; Retain observed
acidification and authors sulfur-oxidation interpretation without MUTUALISM, enzyme/passivation
certainty or the untested sulfur-to-iron feedback.
details: Source-based self-adversarial review; reports/causal_graph_review/decisions/20261007-four-records-batch93.yaml
29 changes: 29 additions & 0 deletions ...ds/Rhizorhabdus_Cupriavidus_BDE47_Degradation_SynCom/2026-10-07T152512Z-codex-2629e0.yaml
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@@ -0,0 +1,29 @@
history_version: 1
target:
kind: record
path: kb/communities/Rhizorhabdus_Cupriavidus_BDE47_Degradation_SynCom.yaml
slug: Rhizorhabdus_Cupriavidus_BDE47_Degradation_SynCom
session:
id: 2026-10-07T152512Z-codex-2629e0
timestamp: '2026-10-07T15:25:12Z'
actors:
- type: ai_agent
name: codex
model: unspecified
agent_tool: codex
links:
issues:
- https://github.com/CultureBotAI/CommunityMech/issues/1751
events:
- type: EDIT
outcome: changed
sections:
- interactions
- discussions
summary: Retain directly supported YL-JM2C-to-JMP134 intermediate CROSS_FEEDING and its
existing downstream direction.; Rename rescue to conversion, remove the unsupported reverse
recipient-to-donor assignment and SYNTROPHY, and qualify the existing endpoint arrow to
intermediate clearance.; Rename the existing consortium endpoint to distinguish parent
disappearance from intermediate accumulation; retain positive removal/bromide evidence
without SYNTROPHY or closed-carbon-balance certainty.
details: Source-based self-adversarial review; reports/causal_graph_review/decisions/20261007-four-records-batch93.yaml
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